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To Change Apache Hadoop MapReduce memory settings:
Available memory to ML Services can be modified when it's running a MapReduce job. To modify a cluster, use the Apache Ambari UI for your cluster. For Ambari UI instructions, see Manage HDInsight clusters using the Ambari Web UI.
Available memory to ML Services can be changed by using Hadoop switches in the call to RxHadoopMR:
hadoopSwitches = "-libjars /etc/hadoop/conf -Dmapred.job.map.memory.mb=6656"
Reference: Azure HDinsight – R Server Overview
Hope this helps.